Another interesting contribute by Dienekes. After having calculated, from the 1KGP, the ages of the most important nodes of the haplogroups, he considers specifically R-M343 and subclades.

“Most times are around 6-7 thousand years ago, but there is an outlier bump at around 15 thousand years ago. To further investigate this bump, I carried out multidimensional scaling of the collection of Y-chromosomes […]It is clear that the group of high pairwise TMRCAs correspond to the individual on the left of the figure that emerges as a clear outlier vis a vis the rest. The ID of that individual is HG00640 (from PUR population). One possibility is that this individual is M343+ due to sequencing error and belongs to a different lineage altogether. However, HG00640 is also R1-S1+ and R1b1-L278+ but R1b1a-P297-.

It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!

The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years”.

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.

Enjoy the new data Maliclavelli, you earned it. It would be great if he could get some of the more "interesting" R1b subclades identified on his pictogram. Based on what we know of the availability of haplotypes, I think the major bumps are the major subclades: P312, U106 and possibly RL21 and U152?

I would guess all the subclades above L11 are the small bumps between 343 and the major subclades? This would support M Heinilas work.

Vincent said... FWIW, most of the Puerto Ricans in the R1b1(xP297) project at FTDNA have Jewish ancestry.

I repeat:

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.

Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

You know that Dienekes is a lover betrayed by STRs, not one who didn’t believe in them from the beginning. But say it to your friend Vincent, who, if the Puerto Rican is a Jew, that’s all right. Unfortunately I have demonstrated to him and to all the others that it isn’t so.

Another interesting contribute by Dienekes. After having calculated, from the 1KGP, the ages of the most important nodes of the haplogroups, he considers specifically R-M343 and subclades.

“Most times are around 6-7 thousand years ago, but there is an outlier bump at around 15 thousand years ago. To further investigate this bump, I carried out multidimensional scaling of the collection of Y-chromosomes […]It is clear that the group of high pairwise TMRCAs correspond to the individual on the left of the figure that emerges as a clear outlier vis a vis the rest. The ID of that individual is HG00640 (from PUR population). One possibility is that this individual is M343+ due to sequencing error and belongs to a different lineage altogether. However, HG00640 is also R1-S1+ and R1b1-L278+ but R1b1a-P297-.

It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!

The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years”.

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.

So we should go with Dienekes age estimate for R1b rather than Karafet's?

Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

You know that Dienekes is a lover betrayed by STRs, not one who didn’t believe in them from the beginning. But say it to your friend Vincent, who, if the Puerto Rican is a Jew, that’s all right. Unfortunately I have demonstrated to him and to all the others that it isn’t so.

It's called cherry picking.

In science

"Choosing to make selective choices among competing evidence, so as to emphasize those results that support a given position, while ignoring or dismissing any findings that do not support it, is a practice known as "cherry picking" and is a hallmark of poor science or pseudo-science. — Richard Somerville, Testimony before the U.S House of Representatives Committee on Energy and Commerce Subcommittee on Energy and Power, March 8, 2011[3]"

Here is an example of cherry picking,

Cohen Modal Haplotype (CMH),J1e and J2a possible Cohen clusters, have R-M429/S2/S22.The same snps found in[IJ] I1 and I2. All Italians with R-M429/S2/S22 are related to both Cohen J1e and J2a CMH, through there paternal line of descent.

Dienekes estimates for R1b's origin are in line with e.g Klyosov for the age of R1b, but his estimate for two subclades of U106 came out to over 6000 years, 2000 years more than what most other estimates have shown...

I am not a statistician or any kind of a mathematician, so I am not qualified to critique this or that approach to estimating the age of this or that haplogroup, but I can make some general observations.

First, I have little faith in these age estimates. They change too often and too radically. The layman gets the impression that none of these people knows what the heck he or she is doing.

Second, they seem to be pretty malleable: one can tailor them to fit his own personal origin theory. And, all too often, one can track or predict origin theories based on the ethnicity of the advocate.

Third, variance doesn't seem to be all that reliable, since a population moving into a new area can be drawn from numerous sources and thus have a higher variance than a population in an older, established region.

So, I'm holding out hope for ancient y-dna findings, but the possibility of contamination worries me a bit.

First, I have little faith in these age estimates. They change too often and too radically. The layman gets the impression that none of these people knows what the heck he or she is doing.

Having spent some time estimating TMRCA myself, I can sympathize with the sentiment. But I think that most credible actors are converging on a small number of refined methods that quite often produce highly concurrent estimates.

This 15kya estimate for the TMRCA of R-L389 is within 1,000 years of two different estimates that I produced using different methods (STR-based variance and SNP counting) almost four years ago.

The academics are still behind in their methodology (mostly their mutation rate assumption), but most credible amateurs are pretty much running in a pack in terms of results even when they are only tangentially coordinating.

Having spent some time estimating TMRCA myself, I can sympathize with the sentiment. But I think that most credible actors are converging on a small number of refined methods that quite often produce highly concurrent estimates.

I think it would help considerably if somebody kept a league table of SNP/clade age estimates showing author attributions (be they academic or credible amateurs) and dates of publication so we could easily see at a glance where the current thinking is.

I have several methods of calculating the time of mutation SNPs (already posted on the forums). Here is one.

According to my calculations (already posted on the forums), one SNP in the approximately 400,000 nucleotides (in WTY)was in about 628 years.In the vertical of ISOGG tree and of Draft Tree (by T.Krahn) be located about 164 SNPs.This gives the time of Adam: 103,000 years

In vertical tree R1b-M343 is average about 30 SNPs. 30 x 628 = 18,840 years.

I have several methods of calculating the time of mutation SNPs (already posted on the forums). Here is one.

According to my calculations (already posted on the forums), one SNP in the approximately 400,000 nucleotides (in WTY)was in about 628 years.In the vertical of ISOGG tree and of Draft Tree (by T.Krahn) be located about 164 SNPs.This gives the time of Adam: 103,000 years

In vertical tree R1b-M343 is average about 30 SNPs. 30 x 628 = 18,840 years.

Stan

Then the 18 SNPs found by Richard Rocca in the 2 Mexican R-U152-s of the 1KGP would mean: 628x18=11,304 years ago.

But probably what makes a mutation to become a SNP is that it is diffused and fixed (and survived) in many close lines and not simply in one unique family.

As with STRs, different SNPs have different mutation rates. That's why some SNPs are seen across many haplogroups and have decimal values (i.e. L69.1, L69.2...). There are lengths in the Y-chromosome that are so unstable, that whatever SNPs are found there are almost useless. That blurs the lines somewhat, as the slowest STRs might be more beneficial for genetic genealogy than the fastest SNPs.

I have a lot of respect for you and your opinions and have always found you to be reliable and unbiased, so I'll take your word for it.

Glad to see you posting here again.

Big fat ditto on that, nice to have somebody with a real grasp of the numbers posting here again too !!!

Yes, VV, would love your perspective. I've got stashes full of long R1b haplotypes all formatted with SNP information. Let me know if there is something I can send you. To be honest, I think some of the things that were forecasted earlier, have just been reaffirmed with the greater depth of data, but you might see some new twists in the data.

for very upstream R1b does look dominated y Jewish names. I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement. Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.

Then the 18 SNPs found by Richard Rocca in the 2 Mexican R-U152-s of the 1KGP would mean: 628x18=11,304 years ago.

SNPs in one sample did not give a good result!

Quote

As with STRs, different SNPs have different mutation rates. That's why some SNPs are seen across many haplogroups and have decimal values (i.e. L69.1, L69.2...)

Do we have something better for dating genealogy?STR is useful, until it does not create a second mutation in the same markers - to about 30 generations.So far we do not know the SNP repeated in the same place and in the same sample.Stan

Does the incorpotation of these very upstream forms of R1b haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.

The age of 15500 years (give or take a millenium or so) should probably be considered in terms of the climatic changes of 14000-9000BC or so which could have had a major impact on human populations and movement.